The 49ers elected to address the offense with their first pick in the NFL draft last spring. Meanwhile, the defense has struggled throughout the first three games of the season, and their starting safeties are banged up and haven’t played well.

Which brings up a pertinent question heading into Week 4 against the Chargers: Will they regret passing on safety Derwin James?

Los Angeles tapped James at No. 17 in April after he was widely considered one of the most promising defensive prospects in the draft after a strong career at Florida State.

So far, James has been one of the best safeties in the NFL while being used all over the field in a Chargers defensive scheme that mirrors San Francisco’s. He has two sacks (which would rank second on the 49ers), an interception (San Francisco has none) and is Pro Football Focus’ No. 7 ranked safety through his first three games.

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“He was a guy that we were very high on,” Kyle Shanahan said. “One of the better safeties that we’ve all personally seen coming out. So, that was very surprising (he fell to No. 17).”

San Francisco is allowing 29.7 points per game, the sixth most in the NFL, and gave up touchdowns on all five of the Kansas City Chiefs’ first-half possessions on Sunday.

The 49ers used their ninth-overall pick on right tackle Mike McGlinchey, who has gotten off to a strong start, particularly while run blocking. He’s expected to replace Joe Staley, 34, on the left side when Staley eventually retires. Tackle is one of the most coveted positions on the field, while safeties have generally been devalued league-wide, evident by the slow free agent market last spring.

Tackle wasn’t a pressing need, as the 49ers had renowned pass protector Trent Brown under contract for one more season. They traded Brown to the New England Patriots after taking McGlinchey and passing on James.

The 49ers brought back safeties Adrian Colbert and Jaquiski Tartt, who are iffy to play Sunday and have struggled.

Colbert left Sunday’s game in Kansas City with a hip injury after dealing with a tweaked hamstring the previous week. Tartt didn’t play against the Chiefs after suffering a shoulder injury late against Detroit on Sept. 16 and hasn’t practiced since. The 49ers gave Tartt a two-year contract extension through 2020 after drafting McGlinchey despite Tartt missing the final seven games of 2017 with a fractured forearm.

While James came in at No. 7 among the 119 safeties graded, Pro Football Focus has Tartt ranked 83rd and Colbert ranked 117th. Colbert has missed five tackles, the second most on the team, while the 49ers lead the NFL with 43 tackles missed.

“He can play in the middle; he can play up at strong safety,” Shanahan said of James. “We thought he was one of the best pass rushers for Florida State. Even a couple of games he played defensive end for a number of plays. So, he’s done it at that versus tackles, he’s done it as a blitzer versus backs and tight ends. So, he’s a very good player.”

“We saw his athletic ability, his skill set, his range, and he’s doing really well,” Chargers coach Anthony Lynn said of James. “He’s a young guy; he’s still learning. He’s a baby. He’s growing each and every day. He’s going to be a heck of a player in this league for a long time.”

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Breida limited in practice —Shanahan said Wednesday he didn’t anticipate running back Matt Breida would practice, but the NFL’s leading rusher wound up being a limited participant in the afternoon session. He left Sunday’s loss in Kansas City momentarily after hyperextending his right knee when his leg got jammed into the turf on a sweeping outside run.

He returned in the third quarter and helped spark the offense with runs of 21 and 27 yards during a touchdown drive. His 274 yards are tied with Cowboys back Ezekiel Elliott to lead the league.

Sherman still in walking boot — Cornerback Richard Sherman remained in a walking boot on his left foot Wednesday and spent the early portion of practice in the team’s weight room. He suffered a calf injury Week 3 and is expected to miss multiple games. Sherman’s absence means the 49ers could be without three of their four starters in the secondary on Sunday.

The 49ers cornerbacks after Sherman left were Jimmie Ward and Ahkello Witherspoon. Ward left the game momentarily after suffering cramps and was replaced by rookie Tarvarius Moore.

Person out again —Right guard Mike Person surprised the 49ers by playing Week 2 despite missing the entire week of practice with a foot injury. Wednesday, he missed practice with a knee injury and worked out on the side field wearing a bulky brace. Erik Magnuson received the early first-team reps at right guard while Joshua Garnett continued his rehab from a dislocated toe suffered Week 1.

▪ Receiver Marquise Goodwin was listed as a limited participant with a quad injury.

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